uploaded (and activated). Thanks!
On Wed, Sep 10, 2014 at 1:14 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Michele - The anatomical segmentation does look good, but from the > screenshot the DWI data seems to be noisy in the orbitofrontal area, which > may be affecting the uncinate. It's hard to tell just from one slice. > > If you upload all the tracula output directories of this subject (dmri, > dmri.bedpostX, dlabel, dpath) for me here, I'll take a look: > https://gate.nmr.mgh.harvard.edu/filedrop2/ > > Thanks! > a.y > > On Wed, 10 Sep 2014, Michele Cavallari wrote: > > Hi Anastasia,I completed the tracula processing. >> By looking at the tractography results in the viewer I noticed that the >> uncinate >> fasciculus is pretty small (see attached screenshot). It actually appears >> as a small >> blue dot. And the problem is both on the left and right side. The other >> tracts look >> fine. I played with threshold, but the size didn't increase. So, I guess >> that something >> wrong happened with the tractography of that particular bundle. I checked >> the aparc+aseg >> output (attached): it seems right to me, but could you please >> double-check? >> Let me also know if you have any suggestions, and if you need more >> information or output >> files. >> Best, >> Michele >> >> Inline image 1 >> >> >> >> On Thu, Sep 4, 2014 at 11:55 PM, Anastasia Yendiki < >> ayend...@nmr.mgh.harvard.edu> wrote: >> >> Hi Ludy - If your gradient table is formatted in 3 rows you need to >> either: >> >> 1. Convert it to 3 columns so you can use it with the 5.3 version of >> tracula, which requires the gradient table to be formatted in >> columns >> >> OR >> >> 2. Download the tracula update that can use gradient tables >> formatted in >> rows >> >> Hope this helps, >> a.y >> >> On Thu, 4 Sep 2014, ls...@bidmc.harvard.edu wrote: >> >> > Hi, >> > >> > I was having similar errors as Michele Cavallari regarding "error >> reading >> /path/to/subject/dmri/dwi_frame," but I'm not sure it's related to >> my bvecs >> file. I did try reconfiguring my bvecs file into columns instead of >> row just >> in case, but that didn't solve the problem. It really just looks >> like it >> can't find the dwi_frame file after the mri_concat command. >> > >> > I am attaching my trac-all.log and config file. >> > >> > Running Freesurfer 5.3 on Macbook OS 10.7.5. The bvecs files were >> generated after I converted my dicoms to nifti using dcm2niigui (GE >> scanner). >> > >> > Can anyone tell me how dwi_frame is generated? >> > >> > >> > Ludy >> > >> > This message is intended for the use of the person(s) to whom it >> may be >> addressed. It may contain information that is privileged, >> confidential, or >> otherwise protected from disclosure under applicable law. If you >> are not the >> intended recipient, any dissemination, distribution, copying, or >> use of this >> information is prohibited. If you have received this message in >> error, >> please permanently delete it and immediately notify the sender. >> Thank you. >> > >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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